* using log directory 'd:/Rcompile/CRANpkg/local/3.3/BioGeoBEARS.Rcheck'
* using R version 3.3.2 (2016-10-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* checking for file 'BioGeoBEARS/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'BioGeoBEARS' version '0.2.1'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'BioGeoBEARS' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' calls to packages already attached by Depends:
  'ape' 'cladoRcpp' 'phylobase' 'rexpokit'
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'ape' 'cladoRcpp' 'methods' 'phylobase' 'rexpokit'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
':::' calls which should be '::':
  'ape:::floating.pie.asp' 'cladoRcpp:::areas_list_to_states_list_old'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
LGcpp_splits_fn_to_table: no visible global function definition for
  'read.table'
LGcpp_splits_fn_to_table2: no visible global function definition for
  'read.table'
LGcpp_states_fn_to_table: no visible global function definition for
  'read.table'
LGpy_splits_fn_to_table: no visible global function definition for
  'read.table'
areas_list_to_states_list_new: no visible global function definition
  for 'numstates_from_numareas'
areas_list_to_states_list_new: no visible global function definition
  for 'rcpp_areas_list_to_states_list'
axisPhylo2: no visible binding for global variable '.PlotPhyloEnv'
axisPhylo2: no visible global function definition for 'axis'
bears_2param_DIVA_fast: no visible global function definition for
  'rcpp_areas_list_to_states_list'
bears_2param_DIVA_fast: no visible global function definition for
  'read.tree'
bears_2param_DIVA_fast : function_to_optim: no visible global function
  definition for 'rcpp_states_list_to_DEmat'
bears_2param_DIVA_fast: no visible global function definition for
  'optim'
bears_2param_DIVA_fast: no visible global function definition for
  'rcpp_states_list_to_DEmat'
bears_2param_standard_fast: no visible global function definition for
  'rcpp_areas_list_to_states_list'
bears_2param_standard_fast: no visible global function definition for
  'read.tree'
bears_2param_standard_fast : function_to_optim: no visible global
  function definition for 'rcpp_states_list_to_DEmat'
bears_2param_standard_fast: no visible global function definition for
  'optim'
bears_2param_standard_fast: no visible global function definition for
  'rcpp_states_list_to_DEmat'
bears_2param_standard_fast_fixnode: no visible global function
  definition for 'rcpp_areas_list_to_states_list'
bears_2param_standard_fast_fixnode: no visible global function
  definition for 'read.tree'
bears_2param_standard_fast_fixnode : function_to_optim: no visible
  global function definition for 'rcpp_states_list_to_DEmat'
bears_2param_standard_fast_fixnode: no visible global function
  definition for 'optim'
bears_2param_standard_fast_fortest: no visible global function
  definition for 'rcpp_areas_list_to_states_list'
bears_2param_standard_fast_fortest: no visible global function
  definition for 'read.tree'
bears_2param_standard_fast_fortest : function_to_optim: no visible
  global function definition for 'rcpp_states_list_to_DEmat'
bears_2param_standard_fast_fortest: no visible global function
  definition for 'optim'
bears_2param_standard_fast_fortest: no visible global function
  definition for 'rcpp_states_list_to_DEmat'
bears_2param_standard_fast_symOnly: no visible global function
  definition for 'rcpp_areas_list_to_states_list'
bears_2param_standard_fast_symOnly: no visible global function
  definition for 'read.tree'
bears_2param_standard_fast_symOnly : function_to_optim: no visible
  global function definition for 'rcpp_states_list_to_DEmat'
bears_2param_standard_fast_symOnly: no visible global function
  definition for 'optim'
bears_2param_standard_fast_symOnly: no visible global function
  definition for 'rcpp_states_list_to_DEmat'
bears_2param_standard_fast_symOnly_simp: no visible global function
  definition for 'rcpp_areas_list_to_states_list'
bears_2param_standard_fast_symOnly_simp: no visible global function
  definition for 'read.tree'
bears_2param_standard_fast_symOnly_simp : function_to_optim: no visible
  global function definition for 'rcpp_states_list_to_DEmat'
bears_2param_standard_fast_symOnly_simp: no visible global function
  definition for 'optim'
bears_2param_standard_fast_symOnly_simp: no visible global function
  definition for 'rcpp_states_list_to_DEmat'
bears_2param_standard_slowQ_slowSP: no visible global function
  definition for 'rcpp_areas_list_to_states_list'
bears_2param_standard_slowQ_slowSP: no visible global function
  definition for 'read.tree'
bears_2param_standard_slowQ_slowSP : function_to_optim: no visible
  global function definition for 'rcpp_states_list_to_DEmat'
bears_2param_standard_slowQ_slowSP: no visible global function
  definition for 'optim'
bears_2param_standard_slowQ_slowSP: no visible global function
  definition for 'rcpp_states_list_to_DEmat'
bears_3param_standard_fast: no visible global function definition for
  'rcpp_areas_list_to_states_list'
bears_3param_standard_fast: no visible global function definition for
  'read.tree'
bears_3param_standard_fast : function_to_optim: no visible global
  function definition for 'rcpp_states_list_to_DEmat'
bears_3param_standard_fast: no visible global function definition for
  'optim'
bears_3param_standard_fast: no visible global function definition for
  'rcpp_states_list_to_DEmat'
bears_3param_standard_fast_fixnode: no visible global function
  definition for 'rcpp_areas_list_to_states_list'
bears_3param_standard_fast_fixnode: no visible global function
  definition for 'read.tree'
bears_3param_standard_fast_fixnode : function_to_optim: no visible
  global function definition for 'rcpp_states_list_to_DEmat'
bears_3param_standard_fast_fixnode: no visible global function
  definition for 'optim'
bears_3param_standard_fast_noJ: no visible global function definition
  for 'rcpp_areas_list_to_states_list'
bears_3param_standard_fast_noJ: no visible global function definition
  for 'read.tree'
bears_3param_standard_fast_noJ : function_to_optim: no visible global
  function definition for 'rcpp_states_list_to_DEmat'
bears_3param_standard_fast_noJ: no visible global function definition
  for 'optim'
bears_3param_standard_fast_noJ: no visible global function definition
  for 'rcpp_states_list_to_DEmat'
bears_4param_standard_fast: no visible global function definition for
  'rcpp_areas_list_to_states_list'
bears_4param_standard_fast: no visible global function definition for
  'read.tree'
bears_4param_standard_fast : function_to_optim: no visible global
  function definition for 'rcpp_states_list_to_DEmat'
bears_4param_standard_fast: no visible global function definition for
  'optim'
bears_4param_standard_fast: no visible global function definition for
  'rcpp_states_list_to_DEmat'
bears_5param_standard_fast: no visible global function definition for
  'rcpp_areas_list_to_states_list'
bears_5param_standard_fast: no visible global function definition for
  'read.tree'
bears_5param_standard_fast : function_to_optim: no visible global
  function definition for 'rcpp_states_list_to_DEmat'
bears_5param_standard_fast: no visible global function definition for
  'optim'
bears_5param_standard_fast: no visible global function definition for
  'rcpp_states_list_to_DEmat'
bears_5param_standard_fast_diffstart: no visible global function
  definition for 'rcpp_areas_list_to_states_list'
bears_5param_standard_fast_diffstart: no visible global function
  definition for 'read.tree'
bears_5param_standard_fast_diffstart : function_to_optim: no visible
  global function definition for 'rcpp_states_list_to_DEmat'
bears_5param_standard_fast_diffstart: no visible global function
  definition for 'optim'
bears_5param_standard_fast_diffstart: no visible global function
  definition for 'rcpp_states_list_to_DEmat'
bears_5param_standard_fast_v: no visible global function definition for
  'rcpp_areas_list_to_states_list'
bears_5param_standard_fast_v: no visible global function definition for
  'read.tree'
bears_5param_standard_fast_v : function_to_optim: no visible global
  function definition for 'rcpp_states_list_to_DEmat'
bears_5param_standard_fast_v: no visible global function definition for
  'optim'
bears_5param_standard_fast_v: no visible global function definition for
  'rcpp_states_list_to_DEmat'
bears_6param_standard_fast_ys_v: no visible global function definition
  for 'rcpp_areas_list_to_states_list'
bears_6param_standard_fast_ys_v: no visible global function definition
  for 'read.tree'
bears_6param_standard_fast_ys_v : function_to_optim: no visible global
  function definition for 'rcpp_states_list_to_DEmat'
bears_6param_standard_fast_ys_v: no visible global function definition
  for 'optim'
bears_6param_standard_fast_ys_v: no visible global function definition
  for 'rcpp_states_list_to_DEmat'
bears_9param_standard_fast_ys_v_cb: no visible global function
  definition for 'rcpp_areas_list_to_states_list'
bears_9param_standard_fast_ys_v_cb: no visible global function
  definition for 'read.tree'
bears_9param_standard_fast_ys_v_cb : function_to_optim: no visible
  global function definition for 'rcpp_states_list_to_DEmat'
bears_9param_standard_fast_ys_v_cb: no visible global function
  definition for 'optim'
bears_9param_standard_fast_ys_v_cb: no visible global function
  definition for 'rcpp_states_list_to_DEmat'
bears_optim_run: no visible global function definition for
  'rcpp_areas_list_to_states_list'
bears_optim_run: no visible global function definition for 'read.tree'
bears_optim_run: no visible global function definition for 'optim'
bears_optim_run: no visible global function definition for
  'rcpp_states_list_to_DEmat'
calc_loglike_for_optim: no visible global function definition for
  'rcpp_states_list_to_DEmat'
calc_loglike_sp: no visible global function definition for 'reorder'
calc_loglike_sp: no visible global function definition for 'mat2coo'
calc_loglike_sp: no visible global function definition for
  'rcpp_calc_anclikes_sp_COOprobs'
calc_loglike_sp: no visible global function definition for
  'rcpp_calc_anclikes_sp_COOweights_faster'
calc_loglike_sp: no visible global function definition for
  'rcpp_calc_rowsums_for_COOweights_columnar'
calc_loglike_sp: no visible global function definition for
  'expokit_dmexpv_Qmat'
calc_loglike_sp: no visible global function definition for
  'rcpp_calc_anclikes_sp'
calc_loglike_sp: no visible global function definition for
  'rcpp_calc_anclikes_sp_using_COOprobs'
calc_loglike_sp: no visible global function definition for
  'rcpp_calc_splitlikes_using_COOweights_columnar'
calc_loglike_sp: no visible global function definition for
  'expokit_dgpadm_Qmat'
calc_loglike_sp_prebyte: no visible global function definition for
  'reorder'
calc_loglike_sp_prebyte: no visible global function definition for
  'mat2coo'
calc_loglike_sp_prebyte: no visible global function definition for
  'rcpp_calc_anclikes_sp_COOprobs'
calc_loglike_sp_prebyte: no visible global function definition for
  'rcpp_calc_anclikes_sp_COOweights_faster'
calc_loglike_sp_prebyte: no visible global function definition for
  'rcpp_calc_rowsums_for_COOweights_columnar'
calc_loglike_sp_prebyte: no visible global function definition for
  'expokit_dmexpv_Qmat'
calc_loglike_sp_prebyte: no visible global function definition for
  'rcpp_calc_anclikes_sp'
calc_loglike_sp_prebyte: no visible global function definition for
  'rcpp_calc_anclikes_sp_using_COOprobs'
calc_loglike_sp_prebyte: no visible global function definition for
  'rcpp_calc_splitlikes_using_COOweights_columnar'
calc_loglike_sp_prebyte: no visible global function definition for
  'expokit_dgpadm_Qmat'
calc_loglike_sp_stratified: no visible global function definition for
  'rcpp_states_list_to_DEmat'
calc_loglike_sp_stratified: no visible global function definition for
  'read.tree'
calc_loglike_sp_stratified: no visible global function definition for
  'mat2coo'
calc_loglike_sp_stratified: no visible global function definition for
  'rcpp_calc_anclikes_sp_COOweights_faster'
calc_loglike_sp_stratified: no visible global function definition for
  'rcpp_calc_rowsums_for_COOweights_columnar'
calc_loglike_sp_stratified: no visible global function definition for
  'reorder'
calc_prob_forward_onebranch_sparse: no visible global function
  definition for 'expokit_dmexpv_Qmat'
chainsaw2: no visible global function definition for 'extract.clade'
chainsaw2: no visible global function definition for 'drop.tip'
check_BioGeoBEARS_run: no visible global function definition for
  'read.tree'
check_BioGeoBEARS_run: no visible global function definition for
  'is.binary.tree'
check_BioGeoBEARS_run: no visible global function definition for
  'numstates_from_numareas'
colors_legend: no visible global function definition for 'plot'
colors_legend: no visible global function definition for 'legend'
cornerlabels: no visible global function definition for 'par'
cornerlabels: no visible global function definition for 'strwidth'
cornerlabels: no visible global function definition for 'strheight'
cornerlabels: no visible global function definition for 'xinch'
cornerlabels: no visible global function definition for 'yinch'
cornerlabels: no visible global function definition for 'rect'
cornerpies: no visible global function definition for 'par'
define_BioGeoBEARS_model_object: no visible global function definition
  for 'new'
define_tipranges_object: no visible global function definition for
  'new'
get_all_daughter_tips_of_a_node: no visible global function definition
  for 'extract.clade'
get_all_node_ages: no visible global function definition for
  'dist.nodes'
get_colors_for_numareas: no visible global function definition for
  'rainbow'
get_colors_for_numareas: no visible global function definition for
  'col2rgb'
get_lagrange_nodenums: no visible global function definition for
  'reorder'
get_node_ages_of_tips: no visible global function definition for
  'dist.nodes'
get_pruningwise_nodenums: no visible global function definition for
  'reorder'
get_statesColors_table: no visible global function definition for
  'rcpp_areas_list_to_states_list'
given_a_starting_state_simulate_branch_end: no visible global function
  definition for 'runif'
given_a_starting_state_simulate_split: no visible global function
  definition for 'rcpp_calc_rowsums_for_COOweights_columnar'
given_a_starting_state_simulate_split: no visible global function
  definition for 'runif'
label_nodes_postorder_phylo3: no visible global function definition for
  'as'
label_nodes_postorder_phylo3: no visible global function definition for
  'reorder'
lrttest: no visible global function definition for 'pchisq'
map_LG_MLsplits_to_tree: no visible global function definition for
  'par'
map_LG_MLsplits_to_tree: no visible global function definition for
  'plot'
map_LG_MLsplits_to_tree: no visible global function definition for
  'nodelabels'
map_LG_MLsplits_to_tree: no visible global function definition for
  'tiplabels'
map_LG_MLsplits_to_tree: no visible global function definition for
  'title'
map_LG_MLsplits_to_tree: no visible global function definition for
  'axisPhylo'
map_LG_MLsplits_to_tree: no visible global function definition for
  'mtext'
map_LG_MLsplits_to_tree_corners: no visible global function definition
  for 'plot'
map_LG_MLsplits_to_tree_corners: no visible global function definition
  for 'axisPhylo'
map_LG_MLsplits_to_tree_corners: no visible global function definition
  for 'mtext'
map_LG_MLsplits_to_tree_corners: no visible global function definition
  for 'tiplabels'
map_LG_MLstates_to_tree: no visible global function definition for
  'plot'
map_LG_MLstates_to_tree: no visible global function definition for
  'axisPhylo'
map_LG_MLstates_to_tree: no visible global function definition for
  'mtext'
map_LG_MLstates_to_tree: no visible global function definition for
  'nodelabels'
map_LG_MLstates_to_tree: no visible global function definition for
  'tiplabels'
map_LGpy_MLsplits_to_tree: no visible global function definition for
  'par'
map_LGpy_MLsplits_to_tree: no visible global function definition for
  'plot'
map_LGpy_MLsplits_to_tree: no visible global function definition for
  'nodelabels'
map_LGpy_MLsplits_to_tree: no visible global function definition for
  'tiplabels'
map_LGpy_MLsplits_to_tree: no visible global function definition for
  'title'
map_LGpy_MLsplits_to_tree: no visible global function definition for
  'axisPhylo'
map_LGpy_MLsplits_to_tree: no visible global function definition for
  'mtext'
mix_colors_for_states: no visible global function definition for 'rgb'
nodenums_bottom_up: no visible global function definition for 'as'
nodenums_bottom_up: no visible global function definition for 'nNodes'
nodenums_bottom_up: no visible global function definition for 'nTips'
nodenums_bottom_up: no visible global function definition for 'nodeId'
parse_lagrange_output: no visible global function definition for
  'write.table'
parse_lagrange_output_old: no visible global function definition for
  'write.table'
parse_lagrange_python_output: no visible global function definition for
  'write.table'
parse_lagrange_python_output_old: no visible global function definition
  for 'write.table'
plot_BioGeoBEARS_model: no visible global function definition for
  'rcpp_areas_list_to_states_list'
plot_BioGeoBEARS_model: no visible global function definition for
  'layout'
plot_BioGeoBEARS_model: no visible global function definition for 'par'
plot_BioGeoBEARS_model: no visible global function definition for
  'plot'
plot_BioGeoBEARS_model: no visible global function definition for
  'text'
plot_BioGeoBEARS_model: no visible global function definition for
  'title'
plot_BioGeoBEARS_model: no visible global function definition for
  'barplot'
plot_BioGeoBEARS_model: no visible global function definition for
  'axis'
plot_BioGeoBEARS_model: no visible global function definition for
  'mtext'
plot_BioGeoBEARS_results: no visible global function definition for
  'read.tree'
plot_BioGeoBEARS_results: no visible global function definition for
  'reorder'
plot_BioGeoBEARS_results: no visible global function definition for
  'numstates_from_numareas'
plot_BioGeoBEARS_results: no visible global function definition for
  'rcpp_areas_list_to_states_list'
plot_BioGeoBEARS_results: no visible global function definition for
  'plot'
plot_BioGeoBEARS_results: no visible global function definition for
  'tiplabels'
plot_BioGeoBEARS_results: no visible global function definition for
  'axisPhylo'
plot_BioGeoBEARS_results: no visible global function definition for
  'mtext'
plot_BioGeoBEARS_results: no visible global function definition for
  'nodelabels'
plot_BioGeoBEARS_results: no visible global function definition for
  'title'
plot_cladogenesis_size_probabilities: no visible global function
  definition for 'rcpp_areas_list_to_states_list'
plot_cladogenesis_size_probabilities: no visible global function
  definition for 'par'
plot_cladogenesis_size_probabilities: no visible global function
  definition for 'plot'
plot_cladogenesis_size_probabilities: no visible global function
  definition for 'title'
plot_cladogenesis_size_probabilities: no visible global function
  definition for 'barplot'
plot_cladogenesis_size_probabilities: no visible global function
  definition for 'axis'
plot_cladogenesis_size_probabilities: no visible global function
  definition for 'mtext'
plot_cladogenesis_size_probabilities: no visible global function
  definition for 'text'
plot_cladogenesis_size_probabilities: no visible global function
  definition for 'rcpp_calc_anclikes_sp_COOweights_faster'
plot_cladogenesis_size_probabilities: no visible global function
  definition for 'rcpp_calc_rowsums_for_COOweights_columnar'
postorder_nodes_phylo4_return_table: no visible global function
  definition for 'is'
postorder_nodes_phylo4_return_table: no visible global function
  definition for 'as'
postorder_nodes_phylo4_return_table: no visible global function
  definition for 'nodeId'
postorder_nodes_phylo4_return_table: no visible global function
  definition for 'descendants'
postorder_nodes_phylo4_return_table: no visible global function
  definition for 'reorder'
prune_specimens_to_species: no visible global function definition for
  'plot'
prune_specimens_to_species: no visible global function definition for
  'axisPhylo'
prune_specimens_to_species: no visible global function definition for
  'title'
prune_specimens_to_species: no visible global function definition for
  'drop.tip'
prune_specimens_to_species: no visible global function definition for
  'is.ultrametric'
read_controls: no visible global function definition for 'read.table'
read_detections: no visible global function definition for 'read.table'
readfiles_BioGeoBEARS_run: no visible global function definition for
  'read.tree'
relative_probabilities_of_subsets: no visible global function
  definition for 'quantile'
relative_probabilities_of_vicariants: no visible global function
  definition for 'median'
relative_probabilities_of_vicariants: no visible global function
  definition for 'quantile'
save_tipranges_to_LagrangePHYLIP: no visible global function definition
  for 'write.table'
section_the_tree: no visible global function definition for 'read.tree'
section_the_tree: no visible global function definition for 'plot'
section_the_tree: no visible global function definition for 'axisPhylo'
simulate_biogeog_history: no visible global function definition for
  'reorder'
simulated_indexes_to_tipranges_object: no visible global function
  definition for 'read.tree'
simulated_indexes_to_tipranges_object: no visible global function
  definition for 'reorder'
traverse_up: no visible global function definition for 'children'
Undefined global functions or variables:
  .PlotPhyloEnv as axis axisPhylo barplot children col2rgb descendants
  dist.nodes drop.tip expokit_dgpadm_Qmat expokit_dmexpv_Qmat
  extract.clade is is.binary.tree is.ultrametric layout legend mat2coo
  median mtext nNodes nTips new nodeId nodelabels
  numstates_from_numareas optim par pchisq plot quantile rainbow
  rcpp_areas_list_to_states_list rcpp_calc_anclikes_sp
  rcpp_calc_anclikes_sp_COOprobs
  rcpp_calc_anclikes_sp_COOweights_faster
  rcpp_calc_anclikes_sp_using_COOprobs
  rcpp_calc_rowsums_for_COOweights_columnar
  rcpp_calc_splitlikes_using_COOweights_columnar
  rcpp_states_list_to_DEmat read.table read.tree rect reorder rgb runif
  strheight strwidth text tiplabels title write.table xinch yinch
Consider adding
  importFrom("grDevices", "col2rgb", "rainbow", "rgb")
  importFrom("graphics", "axis", "barplot", "layout", "legend", "mtext",
             "par", "plot", "rect", "strheight", "strwidth", "text",
             "title", "xinch", "yinch")
  importFrom("methods", "as", "is", "new")
  importFrom("stats", "median", "optim", "pchisq", "quantile", "reorder",
             "runif")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking examples ... [9s] OK
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs